The development of a multicellular organism is achieved by coordinated regulation of cell division, expansion and differentiation. Within each cell, the genetic regulation, which controls development and physiological homeostasis, can be described as a network of permissive and inhibitory interactions between molecules that communicate a biological process or cellular state. Such networks can be characterized by the collection of molecular nodes that are present in the system and by the connections of these nodes by functional interaction. However, the nature of cellular genetic networks is highly dynamic. These networks will change as the cell state progresses through its ontogenic trajectory and as it responds to a changing cellular environment. Multicellular development can thus be described as a system of interconnected cell networks changing over time.
Temporal and spatial gene expression regulation is a primary mechanism that dictates the functional networks underlying physiology and development. Determining the abundance of the RNA and protein expression products of genes in each cell, and through the course of development, may provide quantitative data to model the nodes in these networks. Assigning functional connections between nodes may necessitate additional types of mechanistic data describing the physical interactions between individual RNA, DNA, and protein molecular nodes [Ideker et al. 2001, Harbison et al. 2004, Rual et al. 2005]. Functions ascribed by gene expression regulation at the transcriptional and post-transcriptional level can be achieved by multiple modes of molecular interactions. An understanding of the functional connections regulating expression at a genomic level may include information about transcription factors and the genes they regulate, coordinated regulation of epigenetic states, alternative splicing, and the extent of post-transcriptional regulation.
The root is a plant's primary interface with the environment for nutrition and hydration. However, the root is typically hidden from view and has remained an underexploited target of research in fields such as crop improvement. The sessile nature of plants requires that a plant adapt its developmental program to accommodate its environment. Extensive expression analyses of whole plants or organs exposed to abiotic stimuli have been performed, providing an indication of the genes mediating a response [Seki et al. 2002, Schmid et al. 2005, data publicly available at http://www.arabidopsis.org/info/expression/ATGenExpress.jsp]. However it is understood that the collection of tissue types in each sample may dilute the expression signal from any one tissue [Birnbaum et al. 2003]. It is not generally well understood how each cell type in the root coordinates the genetic response to a change in its environment.
Green Fluorescent Protein (GFP) and other fluorescent proteins may be used for an extensive list of in vivo experimental techniques (see reviews by Giepmans et al. 2006, Dixit and Gilroy 2006). Microscopy images of tissues expressing fluorescent reporters may be a rich form of experimental evidence. Such images may yield quantifiable data for both morphology and for the abundance of fluorescence emission [reviewed by Andrews et al. 2002]. Fusing proteins to GFP has been used to approximate the stoichiometry of interacting proteins in the contractile ring of the single-celled fission yeast [Wu and Pollard 2005]. Work in the single-celled bacteria Escheria coli has demonstrated that capturing the fluorescent activity of promoter reporters by image analysis can predict the order of a genetic pathway and can provide kinetic parameters to quantitatively model a transcriptional network [Kalir et al. 2001, Friedman et al. 2005, Rosenfeld et al. 2005]. Quantitative imaging of promoter reporters in multicellular organisms aims to extract data for each cell or tissue type; however, this work may be complicated by the attenuation and scatter of fluorescence by imaging depth.
Quantitative fluorescence imaging in the root has been performed, such as automating the measurement of relative fluorescence values between tissues layers [Lee et al. 2005, Mace et al (2006)]. However, plants that are grown for root imaging, such as Arabidopsis, are typically transferred from the growth media (e.g., on a Petri dish) to a glass microscopy slide. This process often inflicts damage to the root, and precludes the possibility of unperturbed development upon return to its growth media.